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Nucleic Acids Research, 2000, Vol. 28, No. 24 4944-4955
© 2000 Oxford University Press

Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide

Riccardo Nifosì, Carolina M. Reyes1 and Peter A. Kollman1,*

Scuola Normale Superiore and Istituto Nazionale di Fisica della Materia, Piazza dei Cavalieri 7, 56126 Pisa, Italy and 1Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143-0446, USA

The dynamic behavior of HIV-1 TAR and its complex with argininamide is investigated by means of molecular dynamics simulations starting from NMR structures, with explicit inclusion of water and periodic boundary conditions particle mesh Ewald representation of the electrostatic energy. During simulations of free and argininamide-bound TAR, local structural patterns, as determined by NMR experiments, were reproduced. An interdomain motion was observed in the simulations of free TAR, which is absent in the case of bound TAR, leading to the conclusion that the free conformation of TAR is intrinsically more flexible than the bound conformation. In particular, in the bound conformation the TAR–argininamide interface is very well ordered, as a result of the formation of a U·A·U base triple, which imposes structural constraints on the global conformation of the molecule. Free energy analysis, which includes solvation contributions, was used to evaluate the influence of van der Waals and electrostatic terms on formation of the complex and on the conformational rearrangement from free to bound TAR.

* To whom correspondence should be addressed. Tel: +1 415 476 4637; Fax: +1 415 502 1411; Email: pak{at}cgl.ucsf.edu


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